The incident happened on Friday when police checked the papers of Magomed Tolboyev, who holds the title of a Hero of Russia, in the subway in the southwest of the city.
Taking offence at his appearance and Chechen-sounding name, the two police proceeded to beat up the one-time test pilot and verbally abuse him.
Police have opened an inquiry.
The incident raises further concerns about the risk of racially-motivated attacks in the Russian capital after the school hostage tragedy in the southern Russian town of Beslan, which was blamed on rebels from the Caucasus republics of Ingushetia and Chechnya.
Earlier this week one person was killed and two injured when a group of young skinheads set fire to and gutted Armenian and Azeri restaurants in the Urals city of Ykaterinburg.